Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

Penton, C. Ryan; Gupta, Vadakattu V.  S.  R.; Yu, Julian; Tiedje, James M.

doi:10.3389/fmicb.2016.00824

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

Journal Article · Thu Jun 02 04:00:00 EDT 2016 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2016.00824· OSTI ID:1280873

Penton, C. Ryan ^[1]; Gupta, Vadakattu V. S. R. ^[2]; Yu, Julian ^[3]; Tiedje, James M. ^[4]

Arizona State Univ., Mesa, AZ (United States); Arizona State Univ., Mesa, AZ (United States). Faculty of Science and Mathematics, College of Integrative Sciences and Arts
CSIRO Agriculture, Glen Osmond, SA (Australia)
Arizona State Univ., Mesa, AZ (United States)
Michigan State Univ., East Lansing, MI (United States). Center for Microbial Ecology

We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5, and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI) were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs) retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

View Accepted Manuscript (DOE)

Research Organization:: Arizona State Univ., Mesa, AZ (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0004601

OSTI ID:: 1280873

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 7; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

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